Alain-Fournier was born in La Chapelle-d'Angillon, in the Cher département, in central France, the son of a school teacher. He studied at the Lycée Lakanal in Sceaux, Hauts-de-Seine, near Paris, where he prepared for the entrance examination to the École Normale Supérieure, but without success. He then studied at the merchant marine school in Brest. At the Lycée Lakanal he met Jacques Rivière, and the two became close friends. In 1909, Rivière married Alain-Fournier's younger sister Isabelle.

He interrupted his studies in 1907 and from 1908 to 1909 he performed his military service. At this time he published some essays, poems and stories which were later collected and re-published under the name Miracles.

Throughout this period he was mulling over what would become his celebrated novel, Le Grand Meaulnes. On the first of June 1905, Ascension day, while he was talking a stroll along banks of the Seine he had met Yvonne de Quiévrecourt, with whom he became deeply enamoured. The two spoke, but he did not manage to win her favours. The following year on the same day he waited for her at the same place, but she did not appear. That night he told Rivière, "She did not come. And even if she had, she would not have been the same". They did not meet again until eight years later, when she was married with two children. Yvonne de Quiévrecourt would become Yvonne de Galais in his novel.

He returned to Paris in 1910 and became a literary critic, writing for the Paris-Journal. There he met André Gide and Paul Claudel. In 1912, he quit his job to become the personal assistant of the politician Casimir Perrier. Le Grand Meaulnes was finished in early 1913, and was first published in the Nouvelle Revue Française (from July to October 1913), and then as a book. Le Grand Meaulnes was nominated for, but did not win, the Prix Goncourt. It is available in English in a widely-admired 1959 translation by Frank Davison for Oxford University Press.

In 1914, Alain-Fournier started work on a second novel, Colombe Blanchet, but this remained unfinished when he joined the army as a Lieutenant in August. He died fighting near Vaux-lès-Palameix (Meuse) one month later, on the 22nd of September 1914. His body remained unidentified until 1991, at which time he was interred in the cemetery of Saint-Remy-la-Calonne.

Most of the writing of Alain-Fournier was published posthumously: Miracles (a volume of poems and essays) in 1924, his correspondence with Jacques Rivière in 1926 and his letters to his family in 1930. His notes and sketches for Colombe Blanchet have also been published.

A correspondence between Alain-Fournier and an unidentified woman was found in the Albin Schram Collection. It is a grateful letter for her introduction to Monsieur Hébrard and refers to his next work:

Il m'a proposé pour le Temps ce qu'il était le plus logique de me proposer: lui apporter mon prochain roman - ce que j'ai promis bien volontiers. Ce second roman est, pour l'instant un peu retardé par une nouvelle oeuvre qui s'est mise au travers de ma route et qui ne me laisse pas beaucoup de répit. Mais j'espère bien avant la fin de l'année avoir terminé Colombe Blanchet.

He has proposed to me for Le Temps that which was the most logical thing to propose to me: to bring him my next novel - which I have promised quite willingly. This second novel is, for the moment, somewhat delayed by a new work which is placing itself across my path and which doesn't leave me much respite. But I hope well before the end of the year to have finished Colombe Blanchet.